+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-0964 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of a pre-60S ribosomal subunit - state preA | |||||||||
![]() | Cryo-em structure of a human pre-60S ribosomal subunit state - preA | |||||||||
![]() |
| |||||||||
![]() | 60S / pre-60S / pre-ribosome / human 60S / human pre-ribosome / NMD3 / human NMD3 / RIBOSOME | |||||||||
Function / homology | ![]() negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / basal RNA polymerase II transcription machinery binding / : / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation ...negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / basal RNA polymerase II transcription machinery binding / : / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / axial mesoderm development / ribosomal protein import into nucleus / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / GAIT complex / A band / TORC2 complex binding / alpha-beta T cell differentiation / G1 to G0 transition / regulation of cyclin-dependent protein serine/threonine kinase activity / middle ear morphogenesis / regulation of glycolytic process / regulation of reactive oxygen species metabolic process / translation at presynapse / negative regulation of cell-cell adhesion / positive regulation of dendritic spine development / cytoplasmic side of rough endoplasmic reticulum membrane / maturation of 5.8S rRNA / negative regulation of ubiquitin protein ligase activity / homeostatic process / response to aldosterone / negative regulation of DNA replication / macrophage chemotaxis / lung morphogenesis / ribosomal large subunit binding / Protein hydroxylation / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / blastocyst development / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein localization to nucleus / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / ribosomal subunit export from nucleus / protein targeting / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / rough endoplasmic reticulum / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / MDM2/MDM4 family protein binding / cytosolic ribosome / translation initiation factor activity / negative regulation of protein ubiquitination / embryo implantation / cellular response to interleukin-4 / ossification / innate immune response in mucosa / assembly of large subunit precursor of preribosome / DNA damage response, signal transduction by p53 class mediator / negative regulation of cell migration / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / regulation of signal transduction by p53 class mediator / positive regulation of translation / mRNA 3'-UTR binding / skeletal system development / response to insulin / sensory perception of sound / transcription coactivator binding / cellular response to gamma radiation / bone development / cellular response to type II interferon / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / antimicrobial humoral immune response mediated by antimicrobial peptide / rRNA processing / osteoblast differentiation / positive regulation of protein binding / cellular response to UV / antibacterial humoral response Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
![]() | Liang X / Zuo M | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural snapshots of human pre-60S ribosomal particles before and after nuclear export. Authors: Xiaomeng Liang / Mei-Qing Zuo / Yunyang Zhang / Ningning Li / Chengying Ma / Meng-Qiu Dong / Ning Gao / ![]() Abstract: Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which ...Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly events. Here we present four structures of human pre-60S particles isolated through a nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export. These structures reveal locations of a dozen of human factors, including an uncharacterized factor TMA16 localized between the 5S RNA and the P0 stalk. Comparison of these structures shows a progressive maturation for the functional regions, such as peptidyl transferase centre and peptide exit tunnel, and illustrate a sequence of factor-assisted rRNA maturation events. These data facilitate our understanding of the global conservation of ribosome assembly in eukaryotes and species-specific features of human assembly factors. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 38.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 65.4 KB 65.4 KB | Display Display | ![]() |
Images | ![]() | 87.7 KB | ||
Filedesc metadata | ![]() | 16 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 417.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 416.9 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lssMC ![]() 0948C ![]() 0963C ![]() 0978C ![]() 6lqmC ![]() 6lsrC ![]() 6lu8C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-em structure of a human pre-60S ribosomal subunit state - preA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.058 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : Cryo-EM structure of a human pre-60S ribosomal subunit state - preA
+Supramolecule #1: Cryo-EM structure of a human pre-60S ribosomal subunit state - preA
+Macromolecule #1: Nucleolar GTP-binding protein 2
+Macromolecule #3: Nucleolar GTP-binding protein 1
+Macromolecule #5: Eukaryotic translation initiation factor 6
+Macromolecule #6: Probable ribosome biogenesis protein RLP24
+Macromolecule #8: Zinc finger protein 593
+Macromolecule #9: 60S ribosomal protein L3
+Macromolecule #10: 60S ribosomal protein L29
+Macromolecule #11: 60S ribosomal protein L4
+Macromolecule #12: 60S ribosomal protein L30
+Macromolecule #13: 60S ribosomal protein L34
+Macromolecule #14: 60S ribosomal protein L7a
+Macromolecule #15: 60S ribosomal protein L35
+Macromolecule #16: 60S ribosomal protein L9
+Macromolecule #17: 60S ribosomal protein L36
+Macromolecule #18: 60S ribosomal protein L27a
+Macromolecule #19: 60S ribosomal protein L37
+Macromolecule #20: 60S ribosomal protein L11
+Macromolecule #21: 60S ribosomal protein L38
+Macromolecule #22: 60S ribosomal protein L39
+Macromolecule #23: 60S ribosomal protein L13
+Macromolecule #24: Translation machinery-associated protein 16
+Macromolecule #25: 60S ribosomal protein L14
+Macromolecule #26: 60S ribosomal protein L15
+Macromolecule #27: 60S ribosomal protein L13a
+Macromolecule #28: 60S ribosomal protein L36a
+Macromolecule #29: 60S ribosomal protein L37a
+Macromolecule #30: 60S ribosomal protein L17
+Macromolecule #31: 60S ribosomal protein L18
+Macromolecule #32: 60S ribosomal protein L19
+Macromolecule #33: 60S ribosomal protein L18a
+Macromolecule #34: 60S ribosomal protein L21
+Macromolecule #35: 60S ribosomal protein L22
+Macromolecule #36: 60S ribosomal protein L23
+Macromolecule #37: 60S ribosomal protein L23a
+Macromolecule #38: 60S ribosomal protein L26
+Macromolecule #39: 60S ribosomal protein L27
+Macromolecule #40: 60S ribosomal protein L31
+Macromolecule #41: 60S ribosomal protein L32
+Macromolecule #42: 60S ribosomal protein L28
+Macromolecule #43: 60S ribosomal protein L8
+Macromolecule #44: 60S ribosomal protein L35a
+Macromolecule #45: 60S ribosomal protein L6
+Macromolecule #46: 60S ribosomal protein L7
+Macromolecule #47: 60S ribosomal protein L5
+Macromolecule #48: Protein LLP homolog
+Macromolecule #2: 28S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #7: 28S rRNA
+Macromolecule #49: MAGNESIUM ION
+Macromolecule #50: water
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: PDB ENTRY |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10277 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: PROJECTION MATCHING |